Madison was arguing against factions. He said that factions would happen in a democracy, so the only way to minimize the power of factions would be to regulate the effects, by instituting a republican government.

Religion on dollar bills has been determined to be "ceremonial deism." Sort of a, it doesn't establish a religion or prohibit the practice of religion, so we'll allow it as it's merely ceremonial. The 1st Amendment simply protects against a national religion or the prevention of practicing religion.

The US Constitution does not encourage oppression (3/4ths clause, notwithstanding) of the electorate. The whole concept of the US Constitution was to provide a balanced government which did not empower one body with more power than absolutely necessary. Each branch of the government was designed with some power to prevent the others from running amok. (Except for the Supreme Court. it was not empowered with judicial review until Marbury v. Madison, funny that.)

They were escaping rule of a single king with too much power. That is why initially, the Executive Branch was fairly weak. My guess would be many of the Framers might not be happy with the Executive office as it is today, but that's neither here nor there.

Weed legalization is being brought up because it's time. Society has reached a tipping point of people realizing the effects aren't as bad as stated for decades and the potential benefits could be reaped by society as a whole. Factions (political parties, interest groups) aren't necessarily created like your question seems to assume. An issue arises, different individuals/groups take a particular position, and ally with others to achieve a common goal.

All of that being said, I would say you are off base. Madison warned against factions. He emphasized the importance to scare people into supporting a strong Constitution, with a Bill of Rights. The Constitution was written to break apart the power among representative branches, not to give power to the people.

Additionally, I'm not sure this is right for /r/AskHistorians. Maybe..../r/AskSocialScience? or /r/PoliticalScience